Afghan President Hamid Karzai agreed today to a runoff election against his top challenger after a U.N.-backed audit found that he had failed to win more than 50 percent of votes in the fraud-plagued election.

Flanked by Sen. John Kerry, D-Mass., chairman of the Senate Foreign Relations Committee, and U.N. Special Representative Kai Eide, a visibly tired Karzai defused what the U.S. feared would be a crisis if he rejected the Electoral Complaints Commission report. Instead, Karzai declared the runoff legal and constitutional.

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Earlier this week, the ECC threw out more than 1.3 milllion votes cast on Aug. 20 as fraudulent. Most of those votes -- 1 milliion of them, according to Democracy International -- had been marked for Karzai and made up one-third of Karzai's total. The reduction brought Karzai's tally to 48.3 percent, Democracy International claimed. Those figures were confirmed to ABC News by election officials.

The IEC has questioned the U.N. commission's findings, claiming that Karzai's tally was 49.67 percent – a number that still triggers a runoff but is higher than the count by the ECC.

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"Although the IEC has some reservations," the group said in a statement, "considering the time constraints, the imminent arrival of winter and existence of the problems in the country...the second round of the elections will be held."

Karzai will now face off against his top challenger, Abdullah Abdullah, in a Nov. 7 runoff.

Karzai told the war-battered nation in a televised address that "1.3 million votes were decided to be suspicious. Most of which – around 1 million – were from southern Afghanistan. I call upon our nation to change this into a nation to strengthen our resolve and participate in the new round of elections."

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Karzai's decision ends days of speculation that he or the IEC might reject the commission's findings and refuse a runoff, creating an impasse in the Afghan government and further complicating the Obama administration's Afghan strategy.

President Obama, whose administration has been pressuring Karzai to agree to a runoff, praised the Afghan president.

"President Karzai's constructive actions established an important precedent for Afghanistan's new democracy," Obama said. "The Afghan Constitution and laws are strengthened by President Karzai's decision, which is in the best interests of the Afghan people. "

Obama called Karzai personally to express his appreciation for accepting certification of the Aug. 20 voting results. He also made calls to Abdullah and U.S. ambassador to Afghanistan Karl Eikenberry.

Kerry said of the news, "A moment of great uncertainly has been transformed into a moment of great opportunity." He praised Karzai for what he called "genuine leadership."

"His agreement to move the process forward with respect to the runoff will allow the national leadership to rule with legitimacy," Kerry said. "Dr. Abdullah Abdullah has made the same decision. Both have made their commitment to building a lasting democracy."

Kerry and French Foreign Minister Bernad Koucher have been in Kabul urging the Afghans to resolve the standoff quickly. Kerry met with Karzai five times in five days.

Focus Turns to Second Vote

With the Afghan runoff set for a little more than two weeks from today, preparations for the nationwide vote are now in full swing.